Hey Troubad,
Unfortunately, I think you are correct in that there does not seem to be a way to configure the ASMedia SATA controller in terms of IDE/AHCI mode (and any other relevant options). This is strange considering I was able to configure the 3rd party JMicron SATA controller as AHCI/IDE and other options on my P5B-Deluxe which was a 5+ year old board!
The issue I have experienced is that hotswap does not work properly on the ASMedia ports, I have to power on my eSATA enclosure before booting or the drives will not show up in Windows, and I also cannot safely remove the drives once they are detected in Windows. I haven't experienced the exact issue you are describing, as I only use the ASMedia ports for external eSATA back-up drives. What I would suggest is that if you only have to SATA3 SSDs, connect them both to the two Intel SATA3 ports, and only use the ASMedia ports once you've used all 6 Intel SATA3/2. Even though the ASMedia are SATA3, the performance is not as good as the Intel SATA3 from what I've read (have not tested myself).
It seems like there are issues with the ASMedia implementation on Z77 boards. One thing you can do is post a message on the Hardforum.com forum in the official Asus Z77 support there, as a rep "Raja" can relay issues to Asus HQ. Another option is the official Asus forums, which are horribly laid out and I cannot reliably log into.

Thanks, Grambo, for your thoughtful input. Yes, it looks like ASUS crippled the configuration for the Asmedia SATA3 ports. So it seems that now it will require me to unplug the Asmedia controlled SSD every OS install, or otherwise disable the controller from the BIOS every install. Another negative that goes along with this is that you'd have to re-configure drive order inside Windows every install, because the Asmedia controlled drive will show up with the last drive letter, and the optical drive letter will precede it. Either that or disable both Asmedia and Intel optical drive sata port Either way it's absolutely crazy and unacceptable.

I know about contacting ASUS but to be honest I have lost hope for that. I don't feel they listen or care anyway. They effectively pushed out this lack of features with their Z77 boards without letting anyone know. Do you think I would have bought this board if I could not configure 2 out of 4 Sata3 ports? Hell no. I'm seriously contemplating going back to the Z68 MSI board I have, and doing a ritual burning of this ASUS Maximus V Gene board and taking a vow never to buy ASUS products again. It's a disgrace they tricked people into purchasing these boards. Where can I find the information on the ASUS site or any hardware site that will tell me I cannot configure the SATA3 ports?

BTW, I was also able to configure ports on the ASUS P8Z68 Deluxe board I have, and any other board that make any sense. And yes, the Asmedia controlled drives don't perform as well as the Intel controlled ones, I tested that the other day. Since I have most of my applications (not to mention Window itself) on the Intel controlled SSD I can make full use of its speed. The SSD connected to the Asmedia port I wanted to use for sysprep, vm's, building images, etc. If ASUS will not expand the BIOS for these boards to include configuration options for the Asmedia controllers they have lost my loyalty and respect.

This Max V Gene board also is having many problems with USB devices. And in my case I cannot get it to activate my monitor again after it times out. I have used the same graphics card and monitor on both the P8Z68 board and the MSI Z68 matx board with same graphics drivers and never had any such issue. After the monitor powers down after 20 minutes, and I come back to the PC, whatever I do I cannot get the monitor to come back on. Let me rephrase that: the monitor led changes color (indicating it's active) but the screen remains black. The other day even a manual reset wouldn't work, and I had to force shutdown the PC and then boot again. Then the graphics came back.

I spent $200 on this piece of crap board and their BIOS is not only crippled but completely immature. How dare they release this to their customers like this? I'm not even mad anymore, I feel like a fool for having used my hard-earned cash on a company like this.

I seem to have a problem I've not seen discussed. I installed W7 x64 (SP1), when I got my Asus P8Z77-V Pro without issue, I wanted to reinstall after a few days but now I have a problem. Before the installation can locate the drive I get this error: "A required CD/DVD drive device driver is missing" Windows Installation Error

Now the system drive is the same M4 SSD, in AHCI mode as before when it installed without any problem. I've googled for this error and it seems to relate to missing device drivers, either AHCI or RAID drivers. As far as can work out all required drivers are already present on the W7 SP1 installation disk, and it installed fine without complaint once already.

I've resolved it now. I tried with the W7 DVD as opposed to a flash drive, and it was going to install fine, so I thought what else I may have done differently. I have a DELL monitor with a built in USB hub, and the flash drive was plugged in here. So when I plugged it direct into the USB connector on the back plate the installation worked this time again.

So it was because the flash drive was plugged via the DELL hub that this error came up, direct into the USB 2 on the back plate and all is good. I know I've installed windows many times via that hub, though not on this board.

Sometimes when I cold boot my computer after being shutdown for a long time it reboots itself during startup without even going to POST. I hear the fan speed up, then it reboots and the fan speeds up again.

Usually when I boot my computer I see the message from my GPU(displaying GPU-bios version and so on), later on it goes to the Asus logo/POST. I don't even see the Asus logo or the GPU-info text when I encounter the issue described above. After the reboot it boots without any problem. And it seems like it happens randomly, it does not display any error message and I checked my boot priority. Running the latest BIOS for my Asus p8z77-v Pro. Any tips about this or should I just ignore it?

Thanks, Grambo, for your thoughtful input. Yes, it looks like ASUS crippled the configuration for the Asmedia SATA3 ports. So it seems that now it will require me to unplug the Asmedia controlled SSD every OS install, or otherwise disable the controller from the BIOS every install. Another negative that goes along with this is that you'd have to re-configure drive order inside Windows every install, because the Asmedia controlled drive will show up with the last drive letter, and the optical drive letter will precede it. Either that or disable both Asmedia and Intel optical drive sata port Either way it's absolutely crazy and unacceptable.
I know about contacting ASUS but to be honest I have lost hope for that. I don't feel they listen or care anyway. They effectively pushed out this lack of features with their Z77 boards without letting anyone know. Do you think I would have bought this board if I could not configure 2 out of 4 Sata3 ports? Hell no. I'm seriously contemplating going back to the Z68 MSI board I have, and doing a ritual burning of this ASUS Maximus V Gene board and taking a vow never to buy ASUS products again. It's a disgrace they tricked people into purchasing these boards. Where can I find the information on the ASUS site or any hardware site that will tell me I cannot configure the SATA3 ports?
BTW, I was also able to configure ports on the ASUS P8Z68 Deluxe board I have, and any other board that make any sense. And yes, the Asmedia controlled drives don't perform as well as the Intel controlled ones, I tested that the other day. Since I have most of my applications (not to mention Window itself) on the Intel controlled SSD I can make full use of its speed. The SSD connected to the Asmedia port I wanted to use for sysprep, vm's, building images, etc. If ASUS will not expand the BIOS for these boards to include configuration options for the Asmedia controllers they have lost my loyalty and respect.
This Max V Gene board also is having many problems with USB devices. And in my case I cannot get it to activate my monitor again after it times out. I have used the same graphics card and monitor on both the P8Z68 board and the MSI Z68 matx board with same graphics drivers and never had any such issue. After the monitor powers down after 20 minutes, and I come back to the PC, whatever I do I cannot get the monitor to come back on. Let me rephrase that: the monitor led changes color (indicating it's active) but the screen remains black. The other day even a manual reset wouldn't work, and I had to force shutdown the PC and then boot again. Then the graphics came back.
I spent $200 on this piece of crap board and their BIOS is not only crippled but completely immature. How dare they release this to their customers like this? I'm not even mad anymore, I feel like a fool for having used my hard-earned cash on a company like this.

Good to at least know that the option for 3rd party config was present on the Z68 Deluxe, looks like that one used a Marvell controller (and a JMicron for the eSATA ports). I'm going to ask Asus about this via their forum and Raja but I doubt it will go anywhere, they were not helpful regarding my issue with hotswap not working correctly on the ASMedia ports.